Hi, I have been using LimmaGUI for a while, and I am starting to use Limma directly, and I was comparing the results I get with both methods, to make sure I am doing things right. The lists of genes I am getting are roughly the same, but the orders do change a bit, and so do the B values (that I use to rank the genes). Is this expected, perhaps because different limma versions do calculations in slightly different ways? or is that an indication that I am not doing the analysis in the same way? For LimmaGUI, I use the latest (July 2005), version 1.3.9 (which uses limma 2.0.2) on R 2.1.1 Limma, I am using version 2.2.0 with R 2.2.0 (both latest) In one experiment (two slides only) I get a B max of 6.33 with limma, and 6.92 with LimmaGUI. Another 3.13 with limma, and 2.84 with LimmaGUI. Then I add another 3 slides (5 total now) and the B max increases to 13.0 in both limma and limmaGUI. So, the differences are not big... is this due to slight changes in the way successive versions of limma do certain calculations? The analysis included: - bkg correction: substract - within arrays normalisation: loess print-tip - between arrays normalisation: scale - least squares (for linear model) in limmaGUI (default in limma) Thanks for your help, Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK